Using Compositing for Semi-transparent object effect
Set up the Exclude layers section on each renderlayer so that layers you don't want included in the renderlayer are explicitly excluded:



By default, as you have noticed, objects outside the included layers will still affect the output through indirect lighting/shadows.

This is often very useful when compositing different parts of a scene together which should appear to integrate together seamlessly, but if you don't want this, it can be disabled via the exclude option.  

"Excluded" layers will not have any affect on the output of the renderlayer.